Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups

@article{Goloboff2009PhylogeneticAO,
  title={Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups},
  author={Pablo A. Goloboff and Santiago Andr{\'e}s Catalano and J. Marcos Mirande and Claudia A Szumik and J. Salvador Arias and Mari K{\"a}llersj{\"o} and James S Farris},
  journal={Cladistics},
  year={2009},
  volume={25}
}
Obtaining a well supported schema of phylogenetic relationships among the major groups of living organisms requires considering as much taxonomic diversity as possible, but the computational cost of calculating large phylogenies has so far been a major obstacle. We show here that the parsimony algorithms implemented in TNT can successfully process the largest phylogenetic data set ever analysed, consisting of molecular sequences and morphology for 73 060 eukaryotic taxa. The trees resulting… 

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References

SHOWING 1-10 OF 265 REFERENCES

Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics.

A molecular phylogeny of annelids

Parsimony analyses of annelids based on the largest taxon sample and most extensive molecular data set yet assembled suggest that the poor resolution in the basal parts of the trees presented here may be due to lack of signal connected to incomplete data sets, rapid radiation events and/or uneven evolutionary rates and long‐branch attraction.

Broadly sampled multigene trees of eukaryotes

The analytical approach substantiates the power of increased taxon sampling in placing diverse eukaryotic lineages within well-supported clades and indicates that the six supergroup hypothesis of higher-level eucaryotic classification is likely premature.

Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns

Phylogenetic trees from multiple methods provide strong support for the position of Amborella as the earliest diverging lineage of flowering plants, followed by Nymphaeales and Austrobaileyales, and the plastid genome trees also provide strongSupport for a sister relationship between eudicots and monocots, and this group is sister to a clade that includes Chloranthales and magnoliids.

Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences

A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18S rDNA, rbcL, and atpB representing a total of 4733 bp is presented, resulting in the most highly resolved and strongly supported topology yet obtained for angiosPerms.

Support, Ribosomal Sequences and the Phylogeny Of The Eukaryotes

Trees from aligned sequences from eukaryotes in the Ribosomal Database Project are calculated using parsimony jackknifing which uses a resampling procedure to rapidly search large data sets for the branches that are strongly supported and eliminates poorly supported groups.

A kingdom-level phylogeny of eukaryotes based on combined protein data.

The sequences of four of the most broadly taxonomically sampled proteins available are combined to create a roughly parallel data set to that of SSU rRNA, showing strong support for most major groups and several major supergroups.

The Diversity of Eukaryotes

This catalog includes all known major elements of the comprehensive evolutionary tree of protists and eukaryotes and introduces the concept of “extended in‐group” to refer to in‐groups and the most proximate sister group and to assist in identifying the hierarchical location of taxa.
...